Mercurial > repos > iuc > samtools_markdup

comparison samtools_markdup.xml @ 9:d70e33322da3 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
author iuc
date Sun, 08 Sep 2024 03:22:51 +0000
parents 95b3cda386a2
children
comparison
equal deleted inserted replaced
8:95b3cda386a2 9:d70e33322da3
1 <tool id="samtools_markdup" name="Samtools markdup" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@" > 1 <tool id="samtools_markdup" name="Samtools markdup" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" >
2 <description>marks duplicate alignments</description> 2 <description>marks duplicate alignments</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
49 #end if 49 #end if
50 coordsort.sam 50 coordsort.sam
51 '$output' 51 '$output'
52 ]]></command> 52 ]]></command>
53 <inputs> 53 <inputs>
54 <param name="bamfile" type="data" format="sam,bam,cram" optional="false" label="Alignment" /> 54 <param name="bamfile" type="data" format="sam,unsorted.bam,cram" optional="false" label="Alignment" />
55 <param name="remove" type="boolean" argument="-r" truevalue="-r" falsevalue="" label="Remove duplicate reads" /> 55 <param name="remove" type="boolean" argument="-r" truevalue="-r" falsevalue="" label="Remove duplicate reads" />
56 <param name="supp" type="boolean" argument="-S" truevalue="-S" falsevalue="" label="Mark supplementary reads of duplicates as duplicates" /> 56 <param name="supp" type="boolean" argument="-S" truevalue="-S" falsevalue="" label="Mark supplementary reads of duplicates as duplicates" />
57 <param name="existing_tags" type="boolean" argument="-c" truevalue="-c" falsevalue="" label="Clear previous duplicate settings and tags." /> 57 <param name="existing_tags" type="boolean" argument="-c" truevalue="-c" falsevalue="" label="Clear previous duplicate settings and tags." />
58 <param name="maxlen" type="integer" optional="true" argument="-l" min="0" label="Expected maximum read length of INT bases. (default 300, min=0)"/> 58 <param name="maxlen" type="integer" optional="true" argument="-l" min="0" label="Expected maximum read length of INT bases. (default 300, min=0)"/>
59 <param name="odist" type="integer" optional="true" argument="-d" min="1" label="Optical distance (if set, marks with dt tag, min=1)"/> 59 <param name="odist" type="integer" optional="true" argument="-d" min="1" label="Optical distance (if set, marks with dt tag, min=1)"/>
106 <param name="remove" value="-r" /> 106 <param name="remove" value="-r" />
107 <output name="output" file="2_remove_dups.expected.bam" ftype="bam" lines_diff="4" /> 107 <output name="output" file="2_remove_dups.expected.bam" ftype="bam" lines_diff="4" />
108 </test> 108 </test>
109 <!-- 3) --> 109 <!-- 3) -->
110 <test expect_num_outputs="1"> 110 <test expect_num_outputs="1">
111 <param name="bamfile" value="3_mark_supp_dup.bam" ftype="bam" /> 111 <param name="bamfile" value="3_mark_supp_dup.bam" ftype="bam" />
112 <param name="supp" value="-S" /> 112 <param name="supp" value="-S" />
113 <output name="output" file="3_mark_supp_dup.expected.bam" ftype="bam" lines_diff="4" /> 113 <output name="output" file="3_mark_supp_dup.expected.bam" ftype="bam" lines_diff="4" />
114 <assert_command>
115 <has_text text="samtools sort" negate="true"/>
116 </assert_command>
114 </test> 117 </test>
115 <!-- 4) test stats output --> 118 <!-- 4) test stats output -->
116 <test expect_num_outputs="2"> 119 <test expect_num_outputs="2">
117 <param name="bamfile" value="1_markdup.sam" ftype="sam"/> 120 <param name="bamfile" value="1_markdup.sam" ftype="sam"/>
118 <param name="stats" value="yes" /> 121 <param name="stats" value="yes" />
119 <output name="output" file="1_markdup.expected.bam" ftype="bam" lines_diff="4" /> 122 <output name="output" file="1_markdup.expected.bam" ftype="bam" lines_diff="4" />
120 <output name="stats_output" file="stats.txt" lines_diff="2" /> 123 <output name="stats_output" file="stats.txt" lines_diff="2" />
121 </test> 124 </test>
122 <!-- 5) check that stderr is not swallowed w test data from fixmate --> 125 <!-- 5) check that stderr is not swallowed w test data from fixmate -->
123 <test expect_num_outputs="2" expect_exit_code="1" expect_failure="true"> 126 <test expect_exit_code="1" expect_failure="true">
124 <param name="bamfile" value="3_two_read_mapped.sam" ftype="sam" /> 127 <param name="bamfile" value="3_two_read_mapped.sam" ftype="sam" />
125 <param name="stats" value="yes"/> 128 <param name="stats" value="yes"/>
126 <!-- for some reason this is not possible at the moment
127 <output name="stats_output">
128 <assert_contents>
129 <has_line line="[markdup] error: no MC tag. Please run samtools fixmate on file first."/>
130 </assert_contents>
131 </output> -->
132 <assert_stderr> 129 <assert_stderr>
133 <has_line line="[markdup] error: no MC tag. Please run samtools fixmate on file first."/> 130 <has_line line="samtools markdup: error, no MC tag. Please run samtools fixmate on file first."/>
131 <has_line line="samtools markdup: error, unable to assign pair hash key."/>
134 </assert_stderr> 132 </assert_stderr>
135 </test> 133 </test>
136 <!-- 6) check optical distance and check -c option --> 134 <!-- 6) check optical distance and check -c option -->
137 <test expect_num_outputs="1"> 135 <test expect_num_outputs="1">
138 <param name="bamfile" value="1_markdup.sam" ftype="sam"/> 136 <param name="bamfile" value="1_markdup.sam" ftype="sam"/>
156 <test expect_num_outputs="1"> 154 <test expect_num_outputs="1">
157 <param name="bamfile" value="1_markdup.sam" ftype="sam"/> 155 <param name="bamfile" value="1_markdup.sam" ftype="sam"/>
158 <param name="select_oformat" value="SAM" /> 156 <param name="select_oformat" value="SAM" />
159 <output name="output" file="9_markdup.expected.sam" ftype="sam" lines_diff="4" /> 157 <output name="output" file="9_markdup.expected.sam" ftype="sam" lines_diff="4" />
160 </test> 158 </test>
161 <!-- 10) test cram format --> 159 <!-- 10) essentially the same as test 9 (just converted input to sorted bam .. but telling Galaxy its qname sorted)
160 to test qname sorted bam format and ensure that sorting happens in the tool
161 ie. the qname_sorted bam is not converted implicitly -->
162 <test expect_num_outputs="1">
163 <param name="bamfile" value="1_markdup.qname_sorted.bam" ftype="qname_sorted.bam" />
164 <param name="select_oformat" value="SAM" />
165 <output name="output" file="9_markdup.expected.sam" lines_diff="4" />
166 <assert_command>
167 <has_text text="samtools sort"/>
168 </assert_command>
169 </test>
170
171 <!-- 11) test cram format -->
162 <test expect_num_outputs="1"> 172 <test expect_num_outputs="1">
163 <param name="bamfile" value="10_markdup.sam" ftype="sam"/> 173 <param name="bamfile" value="10_markdup.sam" ftype="sam"/>
164 <param name="select_oformat" value="CRAM" /> 174 <param name="select_oformat" value="CRAM" />
165 <param name="ref_file" value="test.fa" /> 175 <param name="ref_file" value="test.fa" />
166 <output name="output" file="10_markdup.expected.cram" ftype="cram" compare="sim_size" delta="250"/> 176 <output name="output" file="11_markdup.expected.cram" ftype="cram" compare="sim_size" delta="250"/>
177 <assert_command>
178 <has_text text="samtools sort"/>
179 </assert_command>
167 </test> 180 </test>
168 </tests> 181 </tests>
169 <help> 182 <help>
170 Mark duplicate alignments from a coordinate sorted file that has been run through fixmate with the -m option. This program relies on the MC and ms tags that fixmate provides. 183 Mark duplicate alignments from a coordinate sorted file that has been run through fixmate with the -m option. This program relies on the MC and ms tags that fixmate provides.
171 184